MolNFT v1 · #34885 · protein + RNA
Crystal structure of archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase E418N/E420N mutant complexed with trnaopal and O- phosphoserine ("opal complex")
2DU5: “Crystal structure of archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase E418N/E420N mutant complexed with…”. X-ray diffraction, 1 ligand (SEP), 17 pockets (best druggability 0.77). MolNFT v1 #34885 on GenesisL1: 3D structure…
- PDB
- 2DU5
- Type
- protein + RNA
- Length
- 1,070 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA; O-phosphoseryl-tRNA synthetase
- EC
- 6.1.1.-
- UniProt
- O30126
- Ligands
- SEP
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | TRNA | rna | 71 | — | — |
| A | O-phosphoseryl-tRNA synthetase (EC 6.1.1.-) | protein | 534 | 31% helix, 23% strand | O30126 |
| B | O-phosphoseryl-tRNA synthetase (EC 6.1.1.-) | protein | 465 | 33% helix, 26% strand | O30126 |
Ligands and binding sites
- SEP · Phosphoserine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.77 | 0.98 | 18 | empty |
| 2 | 622 | 0.74 | 0.81 | 54 | SEP |
| 3 | 580 | 0.72 | 0.80 | 53 | SEP |
| 4 | 295 | 0.69 | 0.83 | 57 | empty |
| 5 | 891 | 0.68 | 0.75 | 53 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3759 Ų buried · 51 hydrogen bonds · protein-protein
- D–A · 707 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 2DU5 · Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase E418N/E420N… · the same entry in another collection · chain A against A, TM-score 1.00
- O30126 · AlphaFold monomer V2.0 prediction for O-phosphoserine--TRNA(CYS) ligase (O30126) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O30126
- Elsewhere: RCSB PDB 2DU5 · PDBe 2DU5 · UniProt O30126
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